As an approach to the problem of seismic vulnerability evaluation of existing buildings using the predicted vulnerability method, numerical models can be applied to define fragility curves of typical buildings which represent building classes. These curves can be then combined with the seismic hazard to calculate the seismic risk for a building class (or individual buildings). For some buildings types, mainly the unreinforced masonry structures, such fragility analysis is complicated and time consuming if a Finite Element-based method is used. The FEM model has to represent the structural geometry and relationships between different structural elements through element connectivity. Moreover, the FEM can face major challenges to represent large displacements and separations for progressive collapse simulations. Therefore, the Applied Element Method which combines the advantages of FEM with that of the Discrete Element Method in terms of accurately modelling a deformable continuum of discrete materials is used in this paper to perform the fragility analysis for unreinforced masonry buildings. To this end, a series of nonlinear dynamic analyses using the AEM has been per-formed for two unreinforced masonry buildings (a 6-storey stone masonry and a 4-storey brick masonry) using more than 50 ground motion records. Both in-plane and out-of-plane failure have been considered in the damage analysis. The distribution of the structural responses and inter-storey drifts are used to develop spectral-based fragility curves for the five European Macroseismic Scale damage grades.